The first thing you should know is what you can and cannot change(modify).
You can change the ship/station/planet models and names, weapon names and graphics, race names. But you cannot change the in-game ship/race GUI pictures, or add new weapons. There's lots of restrictions with SFC games, so make sure you know exactly what can be done and cannot. I've seen too many people that want to make a mod of xxx, but later only to find the base game engine cannot be modded in desired way.
For example, you want to replace one of the pirates with SW Rebels. But in the end you will still see the pirate pics here and there because they cannot be changed.